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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DOQTL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DOQTL_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DOQTL.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DOQTL/DESCRIPTION’ ... OK
* this is package ‘DOQTL’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DOQTL’ can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'scanOne(y = pheno, x = addcovar, ': unused argument (intcovar = intcovar)
Warning: Package 'DOQTL' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/DOQTL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘genoprob.helper’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assoc.map: no visible binding for global variable ‘sdps’
calc.genoprob2: no visible global function definition for ‘makeCluster’
calc.genoprob2: no visible binding for global variable ‘i’
calc.genoprob2: no visible global function definition for ‘stopCluster’
condense.sanger.snps: no visible global function definition for
‘makeCluster’
condense.sanger.snps: no visible binding for global variable ‘chr’
condense.sanger.snps: no visible global function definition for
‘stopCluster’
convert.genes.to.GRanges: no visible global function definition for
‘metadata<-’
convert.variants.to.GRanges: no visible global function definition for
‘metadata<-’
do.pca: no visible global function definition for ‘impute.knn’
dohap2sanger: no visible global function definition for ‘runValue’
find.overlapping.genes: no visible global function definition for
‘subjectHits’
genoprob.helper: no visible binding for global variable
‘theta.rho.means’
genoprob.helper: no visible binding for global variable
‘theta.rho.covars’
get.chr.lengths: no visible global function definition for ‘seqlengths’
get.snp.details: no visible global function definition for ‘rowRanges’
get.snp.details: no visible global function definition for
‘rowRanges<-’
get.snp.patterns: no visible global function definition for
‘unstrsplit’
get.snp.patterns: no visible global function definition for ‘rowRanges’
impute.genotypes: no visible global function definition for ‘rowRanges’
qtl.qtlrel: possible error in scanOne(y = pheno, x = addcovar, prdat =
prdat, vc = vc, intcovar = intcovar, numGeno = TRUE, test = "None"):
unused argument (intcovar = intcovar)
query.pubmed: no visible binding for global variable
‘org.Mm.egSYMBOL2EG’
query.pubmed: no visible binding for global variable ‘org.Mm.egPMID’
query.pubmed: no visible binding for global variable ‘org.Hs.egPMID’
read.muga.data: no visible binding for global variable ‘MM_geno’
s1.assoc: no visible global function definition for ‘subjectHits’
s1.assoc: no visible global function definition for ‘queryHits’
s1.assoc: no visible global function definition for ‘Rle’
scanone.assoc: no visible global function definition for ‘makeCluster’
scanone.assoc: no visible binding for global variable ‘obj’
scanone.assoc: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
MM_geno Rle chr i impute.knn makeCluster metadata<- obj org.Hs.egPMID
org.Mm.egPMID org.Mm.egSYMBOL2EG queryHits rowRanges rowRanges<-
runValue sdps seqlengths stopCluster subjectHits theta.rho.covars
theta.rho.means unstrsplit
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plot.doqtl.Rd':
‘get.sig.thr()’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘check.do.coat.color’ ‘dof1.trans.probs’ ‘genoprobs2hapblocks’
‘get.diplotype2haplotype.matrix’ ‘get.genotype’ ‘get.haplogroup’
‘get.snp.patterns’ ‘haploprobs2hapblocks’ ‘hs.colors’ ‘hsrat.colors’
‘write.unc.hap.file’
Undocumented data sets:
‘hs.colors’ ‘hsrat.colors’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'add.missing.F1s':
add.missing.F1s
Code: function(founders, snps, sampletype = c("DO", "CC", "DOF1",
"HS", "HSrat", "other"))
Docs: function(founders, snps, sampletype = c("DO", "CC", "DOF1",
"HS", "other"))
Mismatches in argument default values:
Name: 'sampletype' Code: c("DO", "CC", "DOF1", "HS", "HSrat", "other") Docs: c("DO", "CC", "DOF1", "HS", "other")
Codoc mismatches from documentation object 'assoc.map':
assoc.map
Code: function(pheno, pheno.col = 1, probs, K, addcovar, snps, chr,
start, end, model = c("additive", "dominance",
"full"), scan = c("one", "two"), output = c("lod",
"p-value", "bic"), snp.file =
"ftp://ftp.jax.org/SNPtools/variants/mgp.v5.merged.snps_all.dbSNP142.vcf.gz",
cross = c("DO", "CC", "HS"))
Docs: function(pheno, pheno.col = 1, probs, K, addcovar, snps, chr,
start, end, model = c("additive", "dominance",
"full"), scan = c("one", "two"), output = c("lod",
"p-value", "bic"), snp.file =
"ftp://ftp.jax.org/SNPtools/variants/cc.snps.NCBI38.txt.gz")
Argument names in code not in docs:
cross
Mismatches in argument default values:
Name: 'snp.file' Code: "ftp://ftp.jax.org/SNPtools/variants/mgp.v5.merged.snps_all.dbSNP142.vcf.gz" Docs: "ftp://ftp.jax.org/SNPtools/variants/cc.snps.NCBI38.txt.gz"
Codoc mismatches from documentation object 'assoc.plot':
assoc.plot
Code: function(results, mgi.file =
"ftp://ftp.jax.org/SNPtools/genes/MGI.sorted.txt.gz",
highlight, highlight.col = "red", thr, show.sdps =
FALSE, ...)
Docs: function(results, mgi.file =
"ftp://ftp.jax.org/SNPtools/genes/MGI.20130703.sorted.txt.gz",
highlight, highlight.col = "red", thr, show.sdps =
FALSE, ...)
Mismatches in argument default values:
Name: 'mgi.file' Code: "ftp://ftp.jax.org/SNPtools/genes/MGI.sorted.txt.gz" Docs: "ftp://ftp.jax.org/SNPtools/genes/MGI.20130703.sorted.txt.gz"
Codoc mismatches from documentation object 'assoc.scan1':
assoc.scan1
Code: function(pheno, pheno.col, probs, K, addcovar, sdps, markers,
model, output)
Docs: function(pheno, pheno.col, probs, K, addcovar, sdps, snps,
model, output)
Argument names in code not in docs:
markers
Argument names in docs not in code:
snps
Mismatches in argument names:
Position: 7 Code: markers Docs: snps
Codoc mismatches from documentation object 'calc.genoprob':
calc.genoprob
Code: function(data, chr = "all", output.dir = ".", plot = TRUE,
array = c("gigamuga", "megamuga", "muga", "other"),
sampletype = c("DO", "CC", "DOF1", "HS", "HSrat",
"other"), method = c("intensity", "allele"), clust =
c("mclust", "pamk"), founders, transprobs, snps)
Docs: function(data, chr = "all", output.dir = ".", plot = TRUE,
array = c("gigamuga", "megamuga", "muga", "other"),
sampletype = c("DO", "CC", "DOF1", "other"), method =
c("intensity", "allele"), founders, transprobs, snps)
Argument names in code not in docs:
clust
Mismatches in argument names:
Position: 8 Code: clust Docs: founders
Position: 9 Code: founders Docs: transprobs
Position: 10 Code: transprobs Docs: snps
Mismatches in argument default values:
Name: 'sampletype' Code: c("DO", "CC", "DOF1", "HS", "HSrat", "other") Docs: c("DO", "CC", "DOF1", "other")
Codoc mismatches from documentation object 'calc.genoprob.intensity':
calc.genoprob.intensity
Code: function(data, chr, founders, snps, output.dir = ".",
trans.prob.fxn, plot = FALSE, clust = c("mclust",
"pamk"))
Docs: function(data, chr, founders, snps, output.dir = ".",
trans.prob.fxn, plot = FALSE)
Argument names in code not in docs:
clust
Codoc mismatches from documentation object 'convert.allele.calls':
convert.allele.calls
Code: function(geno1, geno2)
Docs: function(geno)
Argument names in code not in docs:
geno1 geno2
Argument names in docs not in code:
geno
Mismatches in argument names:
Position: 1 Code: geno1 Docs: geno
Codoc mismatches from documentation object 'do.trans.probs':
do.trans.probs
Code: function(states, snps, chr = c(1:19, "X"), sex = c("M", "F"),
gen)
Docs: function(states, snps, chr = c(1:19, "X"), sex = c("M", "F"),
do.gen)
Argument names in code not in docs:
gen
Argument names in docs not in code:
do.gen
Mismatches in argument names:
Position: 5 Code: gen Docs: do.gen
Codoc mismatches from documentation object 'do2sanger':
do2sanger
Code: function(do.files, snps, output.file = "do2sanger.txt",
snp.file =
"ftp://ftp.jax.org/SNPtools/variants/mgp.v4.snps.dbSNP.vcf.gz",
return.val = c("numeric", "character"))
Docs: function(do.files, snps, output.file = "do2sanger.txt",
snp.file =
"ftp://ftp.jax.org/SNPtools/variants/cc.snps.NCBI38.txt.gz")
Argument names in code not in docs:
return.val
Mismatches in argument default values:
Name: 'snp.file' Code: "ftp://ftp.jax.org/SNPtools/variants/mgp.v4.snps.dbSNP.vcf.gz" Docs: "ftp://ftp.jax.org/SNPtools/variants/cc.snps.NCBI38.txt.gz"
Codoc mismatches from documentation object 'estimate.cluster.params':
estimate.cluster.params
Code: function(founders, data, chr, clust = c("mclust", "pamk"))
Docs: function(founders, data, chr)
Argument names in code not in docs:
clust
Codoc mismatches from documentation object 'extract.raw.data':
extract.raw.data
Code: function(in.path = ".", prefix, out.path = ".", array =
c("gigamuga", "megamuga", "muga"))
Docs: function(in.path = ".", prefix, out.path = ".", array =
c("megamuga", "muga"))
Mismatches in argument default values:
Name: 'array' Code: c("gigamuga", "megamuga", "muga") Docs: c("megamuga", "muga")
Codoc mismatches from documentation object 'generic.trans.probs':
generic.trans.probs
Code: function(states, snps, chr = "1", sex = c("M", "F"))
Docs: function(states, snps, chr = c(1:19, "X"), sex = c("M", "F"))
Mismatches in argument default values:
Name: 'chr' Code: "1" Docs: c(1:19, "X")
Codoc mismatches from documentation object 'plot.genoprobs':
plot.genoprobs
Code: function(x, snps, colors = "DO", chrlen = "mm10", type =
c("max", "probs"), legend = TRUE, ...)
Docs: function(x, snps, colors = "DO", chrlen = "mm10", ...)
Argument names in code not in docs:
type legend
Mismatches in argument names:
Position: 5 Code: type Docs: ...
write.genoprob.plots
Code: function(path = ".", snps, type = c("max", "probs"))
Docs: function(path = ".", snps)
Argument names in code not in docs:
type
Codoc mismatches from documentation object 'get.mgi.features':
get.mgi.features
Code: function(file =
"ftp://ftp.jax.org/SNPtools/genes/MGI.sorted.txt.gz",
chr = NULL, start = NULL, end = NULL, source =
c("all", "MGI", "VEGA", "ENSEMBL", "Blat",
"NCBI_Gene"), type = c("all", "gene",
"pseudogenic_transcript", "pseudogenic_exon",
"pseudogene", "match", "match-part", "transcript",
"exon", "mRNA", "five_prime_UTR", "start_codon",
"CDS", "stop_codon", "three_prime_UTR",
"pseudogenic_mRNA", "pseudogenic_start_codon",
"pseudogenic_CDS", "pseudogenic_stop_codon",
"pseudogenic_five_prime_UTR",
"pseudogenic_three_prime_UTR", "sequence_feature"))
Docs: function(file =
"ftp://ftp.jax.org/SNPtools/genes/MGI.20140803.sorted.txt",
chr = NULL, start = NULL, end = NULL, source =
c("all", "MGI", "VEGA", "ENSEMBL", "Blat",
"NCBI_Gene"), type = c("all", "gene",
"pseudogenic_transcript", "pseudogenic_exon",
"pseudogene", "match", "match-part", "transcript",
"exon", "mRNA", "five_prime_UTR", "start_codon",
"CDS", "stop_codon", "three_prime_UTR",
"pseudogenic_mRNA", "pseudogenic_start_codon",
"pseudogenic_CDS", "pseudogenic_stop_codon",
"pseudogenic_five_prime_UTR",
"pseudogenic_three_prime_UTR", "sequence_feature"))
Mismatches in argument default values:
Name: 'file' Code: "ftp://ftp.jax.org/SNPtools/genes/MGI.sorted.txt.gz" Docs: "ftp://ftp.jax.org/SNPtools/genes/MGI.20140803.sorted.txt"
Codoc mismatches from documentation object 'get.trans.probs':
get.trans.probs
Code: function(r, do.gen, alpha, chr = "1", sex = c("M", "F"))
Docs: function(r, do.gen, alpha, chr = c(1:19, "X"), sex = c("M",
"F"))
Mismatches in argument default values:
Name: 'chr' Code: "1" Docs: c(1:19, "X")
Codoc mismatches from documentation object 'hmm':
hmm.intensity
Code: function(data, founders, sex, snps, chr, trans.prob.fxn, clust
= c("mclust", "pamk"))
Docs: function(data, founders, sex, snps, chr, trans.prob.fxn)
Argument names in code not in docs:
clust
Codoc mismatches from documentation object 'scanone.assoc':
scanone.assoc
Code: function(pheno, pheno.col, probs, K, addcovar, intcovar,
markers, cross = c("DO", "CC", "HS"), sdp.file, ncl)
Docs: function(pheno, pheno.col, probs, K, addcovar, markers, cross =
c("DO", "CC", "HS"), sdp.file, ncl)
Argument names in code not in docs:
intcovar
Mismatches in argument names (first 3):
Position: 6 Code: intcovar Docs: markers
Position: 7 Code: markers Docs: cross
Position: 8 Code: cross Docs: sdp.file
Codoc mismatches from documentation object 'scanone.perm':
scanone.perm
Code: function(pheno, pheno.col = 1, probs, addcovar, intcovar, snps,
model = c("additive", "full"), path = ".", nperm =
1000, return.val = c("lod", "p"))
Docs: function(pheno, pheno.col = 1, probs, addcovar, intcovar, snps,
model = c("additive", "full"), path = ".", nperm =
1000)
Argument names in code not in docs:
return.val
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'plot.genoprobs':
‘genome’
Undocumented arguments in documentation object 'get.chr.lengths'
‘genome’
Undocumented arguments in documentation object 'interpolate.markers'
‘from’ ‘to’
Bad \usage lines found in documentation object 'condense.sanger.snps':
condense.sanger.snps = function(markers, snp.file, strains, hdf.file, ncl = 1)
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
FAILURE in test_qtlrel_vs_matrixqtl: Error in checkEqualsNumeric(target = qt$lod[, 7], current = fq[, 1], tolerance = 0.1) :
Mean relative difference: 3.600419
Test files with failing tests
test_qtl.R
test_qtlrel_vs_fastqtl
test_qtlrel_vs_matrixqtl
Error in BiocGenerics:::testPackage("DOQTL") :
unit tests failed for package DOQTL
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 5 WARNINGs, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/DOQTL.Rcheck/00check.log’
for details.
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("DOQTL")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
[1] "Retrieved 23114 SNPs."
[1] "Retaining 20706 high quality SNPs."
[1] "Retaining 11156 polymorphic SNPs."
R/QTLRel is loaded
[1] "Mapping with 141 samples."
[1] "Mapping with 537 markers."
[1] "WBC1"
SNP 0
SNP 0
[1] "Mapping with 141 samples."
[1] "Mapping with 537 markers."
[1] "WBC1"
SNP 0
We now use 'E' (not 'EE') for residual variance matrix; see documentation.
Timing stopped at: 4.528 0.827 6.086
Error in checkEqualsNumeric(target = qt$lod[, 7], current = fq$lod[, 7], :
Mean relative difference: 3.531309
In addition: Warning messages:
1: Package 'DOQTL' is deprecated and will be removed from Bioconductor
version 3.10
2: In .vcf_map_samples(samples(hdr), samples) :
samples not in file: 'C57BL_6J'
SNP 0
We now use 'E' (not 'EE') for residual variance matrix; see documentation.
We now use 'E' (not 'EE') for residual variance matrix; see documentation.
[1] "Time: 0.368000000000002 sec."
Timing stopped at: 5.497 1.438 7.635
Error in checkEqualsNumeric(target = qt$lod[, 7], current = fq[, 1], tolerance = 0.1) :
Mean relative difference: 3.600419
RUNIT TEST PROTOCOL -- Wed Oct 16 02:30:39 2019
***********************************************
Number of test functions: 7
Number of errors: 0
Number of failures: 2
1 Test Suite :
DOQTL RUnit Tests - 7 test functions, 0 errors, 2 failures
FAILURE in test_qtlrel_vs_fastqtl: Error in checkEqualsNumeric(target = qt$lod[, 7], current = fq$lod[, 7], :
Mean relative difference: 3.531309
FAILURE in test_qtlrel_vs_matrixqtl: Error in checkEqualsNumeric(target = qt$lod[, 7], current = fq[, 1], tolerance = 0.1) :
Mean relative difference: 3.600419
Test files with failing tests
test_qtl.R
test_qtlrel_vs_fastqtl
test_qtlrel_vs_matrixqtl
Error in BiocGenerics:::testPackage("DOQTL") :
unit tests failed for package DOQTL
Execution halted